Team:TCU Taiwan/M13Phage

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     <td width="68%" align="left" valign="middle"><h6><font face="Trebuchet MS" size="7" color="#484644">Modeling</font></h6></td>
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     <td width="68%" align="left" valign="middle"><h6><font face="Trebuchet MS" size="7" color="#484644">M13 Phage</font></h6></td>
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       <li><a href="https://2014.igem.org/Team:TCU_Taiwan/Team"><font size="3">Team Members</font></a></li>
       <li><a href="https://2014.igem.org/Team:TCU_Taiwan/Team"><font size="3">Team Members</font></a></li>
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      <li><a href="https://2014.igem.org/Team:TCU_Taiwan/Achievements"><font size="3">Achievements</font></a></li>
       <li><a href="https://igem.org/Team.cgi?id=1473" target="_blank"><font size="3">Official Team Profile</font></a></li>
       <li><a href="https://igem.org/Team.cgi?id=1473" target="_blank"><font size="3">Official Team Profile</font></a></li>
       <li><a href="https://2014.igem.org/Team:TCU_Taiwan/Contact"><font size="3">Contact</font></a></li>
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       <li><a href="https://2014.igem.org/Team:TCU_Taiwan/Project"><font size="3">Introduction</font></a></li>
       <li><a href="https://2014.igem.org/Team:TCU_Taiwan/Parts"><font size="3">Parts</font></a></li>
       <li><a href="https://2014.igem.org/Team:TCU_Taiwan/Parts"><font size="3">Parts</font></a></li>
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      <li><a href="https://2014.igem.org/Team:TCU_Taiwan/SystemDesign"><font size="3">System Design</font></a></li>
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      <li><a href="https://2014.igem.org/Team:TCU_Taiwan/M13Phage"  style="color:#DBAC52"><font size="3">M13 Phage</font></a></li>
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      <li><a href="https://2014.igem.org/Team:TCU_Taiwan/CRISPR"><font size="3">CRISPR</font></a></li>
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      <li><a href="https://2014.igem.org/Team:TCU_Taiwan/FutureWorks"><font size="3">Future Works</font></a></li>
       <li><a href="https://2014.igem.org/Team:TCU_Taiwan/HumanPratics"><font size="3">Human Pratics</font></a></li>
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     <td style="background-color:#FFF2B5" height="20"><font face="Trebuchet MS" size="6" color="#A66B38">M13 Phage Mechanism</font></td>
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  <legend class="qnum" align="center"><font face="Trebuchet MS" size="6" color="#0092C7">1.Introduction</font><br>
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<div class="wrapper" style="background-color: white;"><font size="3" face="Verdana" color="#333">TEST.</font></div>
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     <td><font size="3" face="Verdana" color="#333"><p>In our project, the CRISPR system is been transported by phage. So  how can phage recognized which DNA it should package and spread? That is  accessed by phagemid and helper phage.</p></font></td>
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  <legend class="qnum" align="center"><font face="Trebuchet MS" size="6" color="#0092C7">2.Software</font><br>
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<div class="wrapper" style="background-color: white;"><p><font face="Trebuchet MS" size="5" color="#90B849">MATLAB</font><br><br>
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  <p class="qbody" align="justify"><font size="3" face="Verdana" color="#333"><img src="https://static.igem.org/mediawiki/2012/3/3f/MathWorks_logo.png" width="400" height="78" style=" float: right; margin-right: 5px; margin-left: 5px;">MATLAB(<strong>MAT</strong>rix <strong>LAB</strong>oratory) is a high-level language and interactive environment for numerical computation, visualization, and programming. Using MATLAB, you can analyze data, develop algorithms, and create models and applications. The language, tools, and built-in math functions enable you to explore multiple approaches and reach a solution faster than with spreadsheets or traditional programming languages, such as C/C++ or Java™.</font></p>
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<p class="qbody"></p><br><br><br><br><p><font face="Trebuchet MS" size="5" color="#90B849">ANFIS</font><br>
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<font size="3" face="Verdana" color="#333">The architecture and learning procedure underlying ANFIS (<strong>A</strong>daptive <strong>N</strong>etwork-based <strong>F</strong>uzzy <strong>I</strong>nference <strong>S</strong>ystem) is presented, which is a fuzzy inference system implemented in the framework of adaptive networks. By using a hybrid learning procedure, the proposed ANFIS can construct an input-output mapping based on both human knowledge (in the form of fuzzy if-then rules) and stipulated input-output data pairs. In the simulation, the ANFIS architecture is employed to model nonlinear functions, identify nonlinear components on-line in a control system, and predict a chaotic time series, all yielding remarkable results. Comparisons with artificial neural networks and earlier work on fuzzy modeling are listed and discussed.</font></div>
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                <td><img src="https://static.igem.org/mediawiki/2014/b/b8/TCU_M13-1.jpg" width="100%"/></td>
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                <td align="center"><font size="3" face="Verdana"><strong>Fig.1</strong></font></td>
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    <td><font size="3" face="Verdana" color="#333"><p>Take M13KO7 helper phage and phagemid pBluescript II SK(-) as  example, as we use them in our experiment. M13KO7 helper phage has complete  coat proteins and a complete genome just like normal M13 phage. But its f1 ori  has been inserted by a p15A ori and a kanamycin resistance gene. While in  pBluescript, its structure is like a normal plasmid but carries two replication  origin: a high efficient PUC ori for itself, and an additional normal f1 ori. <br />
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    In other phagemid and helper phage pairs, situations are same:  helper phage&rsquo;s replication origin is mutated while phagemid contains an  additional replication origin for this helper phage.</p></font></td>
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<img alt=" change width 586 to 520 & 745 " style="float: left; position: relative; z-index: 2" src="https://static.igem.org/mediawiki/2014/2/28/TCU_M13-2.jpg" onmouseover="this.style.width='745px'" onmouseout="this.style.width='520px'" width="100%"><font size="3" face="Verdana"><strong>Fig.2</strong></font>
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        <td valign="top"><font size="3" face="Verdana" color="#333"><p>When a normal M13 phage infect <em>E.coli</em><em> with </em>F plasmid(strain JM101 in our experiment), it will use F pilus to put its  genome into cytosol. Then this single strand genome will use host&rsquo;s polymerase to make itself a  double strand structure and stay in cytosol like a plasmid. <br /></p>
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<p>M13 genome contains major 9 genes, we call each gene&rsquo;s product as gp1, gp2, etc. When it wants to produce progeny phage, gp2 will recognize f1 ori and make a single  strand break on genome. Then gp5 will form dimer structure and start to package  this single strand DNA from package signal on f1 ori, this will help stabilize  single strand genome in cytosol. After that, progeny phage will be released from host cell and be  coated by gp3, gp6, gp7, gp8, gp9.</p></font></td>
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          <p><font color="#333" size="3" face="Verdana">When it comes to M13KO7 helper phage, it  still can successfully infect <em>E.coli with </em>F plasmid and make its genome stable in cytosol by  host&rsquo;s polymerase. But because its f1 ori has been  mutated, so gp2  cannot make a nick on M13KO7's genome. This means,  helper phage cannot produce progeny phage itself.<br /></font></p>
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          <p><font color="#333" size="3" face="Verdana">However, if this <em>E.coli </em>has  been transformed with a pBluescript II SK(-), gp2 will recognize intergenic region and make a  nick on this plasmid. And then gp5  dimers will package the single strand of pBluescript because they believe this  is their &ldquo;genome&rdquo;! In this situation, host cell will release phages but these  phages do not contains their genome, they will carry phagemid instead. So they  will not be able to make next generation after infection, so we call them &ldquo;phagemid-carrying  phage&rdquo;.</font></p></td>
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        <td width="10">&nbsp;</td>
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<img alt=" change width 586 to 520 & 745 " style="float: right; position: relative; z-index: 2" src="https://static.igem.org/mediawiki/2014/9/9c/TCU_M13-3.jpg" onmouseover="this.style.width='745px'" onmouseout="this.style.width='520px'" width="100%"><font size="3" face="Verdana"><strong>Fig.3</strong></font>
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<p>If you choose to create a model during your project, please write about it here. Modeling is not an essential part of iGEM, but we encourage any and all teams to model some aspect of their project. See previous "Best Model" awards for more information.</p>
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Latest revision as of 21:06, 17 October 2014


 
M13 Phage
  
 
M13 Phage Mechanism
 

In our project, the CRISPR system is been transported by phage. So how can phage recognized which DNA it should package and spread? That is accessed by phagemid and helper phage.
 
Fig.1
 

Take M13KO7 helper phage and phagemid pBluescript II SK(-) as example, as we use them in our experiment. M13KO7 helper phage has complete coat proteins and a complete genome just like normal M13 phage. But its f1 ori has been inserted by a p15A ori and a kanamycin resistance gene. While in pBluescript, its structure is like a normal plasmid but carries two replication origin: a high efficient PUC ori for itself, and an additional normal f1 ori.
In other phagemid and helper phage pairs, situations are same: helper phage’s replication origin is mutated while phagemid contains an additional replication origin for this helper phage.
 
change width 586 to 520 & 745 Fig.2
 

When a normal M13 phage infect E.coli with F plasmid(strain JM101 in our experiment), it will use F pilus to put its genome into cytosol. Then this single strand genome will use host’s polymerase to make itself a double strand structure and stay in cytosol like a plasmid.

M13 genome contains major 9 genes, we call each gene’s product as gp1, gp2, etc. When it wants to produce progeny phage, gp2 will recognize f1 ori and make a single strand break on genome. Then gp5 will form dimer structure and start to package this single strand DNA from package signal on f1 ori, this will help stabilize single strand genome in cytosol. After that, progeny phage will be released from host cell and be coated by gp3, gp6, gp7, gp8, gp9.
 

When it comes to M13KO7 helper phage, it still can successfully infect E.coli with F plasmid and make its genome stable in cytosol by host’s polymerase. But because its f1 ori has been mutated, so gp2 cannot make a nick on M13KO7's genome. This means, helper phage cannot produce progeny phage itself.

However, if this E.coli has been transformed with a pBluescript II SK(-), gp2 will recognize intergenic region and make a nick on this plasmid. And then gp5 dimers will package the single strand of pBluescript because they believe this is their “genome”! In this situation, host cell will release phages but these phages do not contains their genome, they will carry phagemid instead. So they will not be able to make next generation after infection, so we call them “phagemid-carrying phage”.

  
change width 586 to 520 & 745 Fig.3
 
 
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Team Members Project Parts Human Pratics Modeling Safety Notebook Attributions

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